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    <title>Identification - Sirius structure prediction</title>
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    <h1>Sirius Identification module</h1>
    <p>This module allows identification of peaks using Böcker lab tool: Sirius (locally) & FingerId (through Web-API).</p>
    <p>Module processes peaks using two jobs</p>
    <ol>
      <li>
        <h3>Sirius Identification job</h3>
        <p>It is a tool for identification of possible compounds. The result of this job shows compounds' formulas.<br>
        There is a timer for this job, it allows to limit amount of time for processing a peak. Because on some datasets it can compute for too long.</p>
        <p>The results of this job are later proceed to FingerId Web method.</p>
      </li>
      <li>
        <h3>FingerId Identification job</h3>
        <p>FingerId identification job uses results from previous method and makes several web-requests on Böcker lab server.<br>
          You will receive a list of possible candidates per each compound.</p>
        <p>If there is an item with the <b>Sirius score</b>, but without <b>FingerId score</b>, that means the processing of this compound by FingerId did not return any candidates.</p>
        <p>There is internal timer that tracks the status of the job on a web-server. It is not configurable from user side.</p>
      </li>
    </ol>

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      <h2>Single item identification task</h2>
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        <h3>Selection of a peak for identification</h3>
        <img src="singleTaskSelection.JPG">
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        <h3>Dialogue window</h3>
        <img src="SingleTaskDialogue.JPG">
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        <h3>Identification results</h3>
        <img src="SingleTaskResults.JPG">
        <ul>
          <li>Button <b>Add identity</b> - adds new identity.</li>
          <li>Button <b>Copy SMILES string</b> - copies to the clipboard SMILES of selected compound (if it is successfully processed by FingerId).</li>
          <li>Button <b>Copy Formula string</b> - copies to the clipboard Formula value of selected compound.</li>
          <li>Button <b>Display DB links</b> - displays another window with pairs of DB name: ID.</li>
          <li>If mouse hovers a preview image of the compound, large image is shown.</li>
        </ul>
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        <h3>List of DB links returned from FingerId job</h3>
        <img src="SingleTaskDB.JPG">
        <ul>
          <li>Button <b>Open browser</b> - opens a new page about selected pair in a default browser.</li>
        </ul>
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      <hr>
      <h2>Peak list identification task</h2>
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        <h3>Dialogue window</h3>
        <img src="PeakListDialogue.JPG">
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    <h4>Method parameters</h4>
    <dl>
      <dt>Precursor m/z</dt>
      <dd>Detected m/z value of the peak. This is set by default to the peak m/z subjected to identification.</dd>

      <dt>Ionization method</dt>
      <dd>Type of ionization that produced the peak subjected to identification. This is used to calculate the neutral
        mass.</dd>

      <dt>Number of candidates from Sirius method</dt>
      <dd>Limit the amount of top rated results to return from Sirius Identification job.</dd>

      <dt>Number of candidates from FingerId method</dt>
      <dd>Limit for the number of results to be retrieved from FingerId job.<br>
        <b>Remember!</b> Each result from Sirius method produces this number of candidates (if identified by FingerId).</dd>

      <dt>Mass tolerance</dt>
      <dd>Tolerance of the neutral mass for searching the database.</dd>

      <dt>Elements</dt>
      <dd>Elements allowed in the formula and their minimum and maximum counts (values from 0 to 100).</dd>

      <dt>Timer for Sirius Identification job</dt>
      <dd>Amount of seconds provided for Sirius Identification job. If it expires - a dialogue window is shown and task is cancelled.</dd>

      <dt>Amount of parallel jobs</dt>
      <dd>This field allows to speed up the peak list processing using parallelism. You can set the amount of parallel threads.<br>
        Values from 1 to 20 (be careful).</dd>

      <dt>Mass list</dt>
      <dd>The same value of Mass List Name is used for MS1 and MS2 scans<br>
        You have to run Mass Detection module on all scans with the same mass list name in order to use them in module like this.<br>
        Note that the MS1 spectrum can contain the deconvoluted isotopic peaks.</dd>
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